Diversity of Life & Molecular Biology

Diversity of Life

• Life is diverse from single-celled bacteria to multicellular eukaryotes
• Despite diversity, the core molecular features are similar across all organisms
• All living organisms share common descent from the Last Universal Common Ancestor (LUCA)

Common Themes for Living Organisms

• Single or multicellular organisms share conserved core features
• Organisms must separate from their environment via a lipid-based membrane
• Organisms must store information in a stable way using DNA & RNA
• Organisms must replicate and pass information to the next generation through DNA Replication
• Organisms must extract energy from their surroundings via ATP

Four Basic Classes of Building Molecules

• Living organisms are constructed from four basic classes of molecules built from smaller subunits
• Nucleic acids (like DNA and RNA) are made of nucleotides, storing and carrying information
• Proteins are made of amino acids and carry out most of a cell's functions
• Lipids, comprised of fatty acids, form membranes around cells and organelles and are hydrophobic
• Carbohydrates are made of small sugars and have a wide array of roles, they are hydrophilic

Structure of DNA

• DNA (deoxyribonucleic acid) stores information in a stable, heritable form
• DNA comprises four nucleotides: deoxyguanosine monophosphate (G), deoxyadenosine monophosphate (A), deoxythymidine monophosphate (T), and deoxycytidine monophosphate (C)
• The order of nucleotides in DNA is the information 'code'
• DNA forms a double helix with paired nucleotides: A with T, and C with G
• The DNA double helix has directionality ("head (5') to toe (3')")

The Genome: A Working Blueprint for Life

• DNA's two-stranded structure enables separation and copying of information
• Original strands separate
• Nucleotides are added to separated strands to form new, complementary strands (A with T, C with G)
• Two new double-stranded DNA molecules are produced from one original
• All the DNA sequences in an organism form its genome, serving as the blueprint
• RNA (ribonucleic acid) is often single-stranded and primarily used for information transfer

The Genome: A Working Blueprint for Life pt. 2

• Genetic information passes to new cells or generations through genome transmission
• Accurate copying (replication)
• Correct separation (segregation) of copies
• Copies transfer into new cells
• Processes have safety nets and checkpoints

Genome Structure

• Consists largely of genes and intergenic regions
• A gene (coding + regulatory region) controls a hereditary characteristic, usually proteins or RNA
• Genes contain product information plus instructions for production timing and location
• Non-genic "Junk" DNA is proving functional
• DNA is packaged into linear or circular chromosomes
• DNA in eukaryotes wraps around histones for compaction
• Some cells contain extra DNA pieces called plasmids

Gene Number and Genome Size

• Genomes vary widely in terms of size, gene number and spacing
• E. coli is 98%, genic; 98% of the human genome is intergenic
• Single celled organisms typically have fewer genes than multi-cellular organisms
• Larger genome size and complexity do not always correlate with greater complexity
• the single-celled amoeba genome is more than 200x the size of humans
• Genomes often contain transposable elements, which are pieces of DNA that copy themselves within a genome and increase genome size

Gene Expression

• rRNA undergoes RNA processing
• mRNA is translated into protein
• tRNA is involved in transcription
• Gene expression is the flow of biological information

Gene Expression pt. 2

• Genetic information, stored in the genome, must be "expressed" to be functional
• Expression converts genome information into products like RNA or protein
• RNA is made via transcription (copying a genomic region)
• RNA may be used directly by the cell or direct the manufacture of a particular protein

Transcription

• Transcription copies DNA into RNA
• RNA polymerase synthesizes RNA
• DNA regions (initiator and terminator) signal RNA polymerase to start and stop
• RNA replaces thymidine with uracil, which pairs with adenosine
• Coding RNA (mRNA) is translated to protein, while Non-coding RNA is not
• Primary transcripts go through RNA processing to yield final products

Translation

• Messenger RNAs (mRNAs) contain information to produce a protein
• Proteins are built from amino acids
• Twenty amino acids are commonly used (+ selenocysteine, pyrrolysine, formyl-methionine)
• Proteins range from a few amino acids to thousands
• Proteins may have separate domains that form a functional unit
• Translation includes post-translational modification, such as protein cleavage, glycosylation, phosphorylation

Translation Machinery

• Translation turns mRNA information into a protein
• mRNA sequences indicate where translation should begin and end
• Three mRNA nucleotides, called a codon, encode each amino acid
• Translation is performed by the ribosome, which has protein and RNA components
• Transfer RNA (tRNA) interprets mRNA information into protein sequence

Triplets Codons

• Most amino acids can be encoded by multiple codons
• Methionine (codon AUG) indicates the start of a protein
• Stop codons (UAG, UGA, UAA) indicate the end of a protein

Growing Number of Gene Products

• The human genome contains about 20,000 protein-encoding genes
• There are far number of different human products than there are genes
• Small RNAs have recently been discovered

Regulation of Gene Expression

• Regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels
• Regulation occurs at the right time, place, and amount
• Gene expression differs in different tissues with the same genome

Eukaryotic Gene Regulation

• Different morphology and functions in different cells although the genome is identical
• Same genome (collection of genes), but different proteomes (collection of proteins) are found in different cell types
• Gene regulation creates the different cell types within a multicellular organism

Regulation of Gene Expression pt.3

• Gene expression is regulated at transcriptional, post-transcriptional, translational, and post-translational levels
• Control of molecular synthesis, processing, and degradation is key to gene regulation

Regulation of Gene Expression pt.4

• Gene regulation influences different tissue activities
• For example, the Hy5 protein in Arabidopsis controls seedling height; it's present under high light, keeping seedlings short, and degrades in low light, causing seedlings to grow tall

Regulation of Gene Expression pt. 5

• Genes are regulated temporally and spatially
• Spatial expression of an even-skipped gene in Drosophila helps control proper segmentation of the embryo

Genome in Prokaryotes

• Cell components are spatially organized to facilitate functions
• Prokaryotes lack internal membrane-bound compartments; eukaryotes have them
• Prokaryotes have chromosomal DNA concentrated in the nucleoid
• Cytoplasm consists of non-specialized regions

Genome in Eukaryotes

• Eukaryotic compartmentalization is more complex
• Chromosomes reside in the membrane-bound nucleus
• Membrane-bound organelles perform distinct functions
• Mitochondria (energy) and chloroplasts (plants harvesting sunlight) contain their own genomes (endosymbionts, endosymbiosis)
• The endoplasmic reticulum and Golgi apparatus involved in protein production and processing

Benefits of Compartmentalization

• Subcellular compartmentalization confines specialized functions
• Compartmentalization provides extra regulation, for example:
• Eukaryotic transcription occurs in the nucleus
• Translation occurs outside the nucleus

Expression of the Genome

• The activity/interplay of all genes in a cell produces the cell's or organism's phenotype
• Phenotype is the visual expression of genes
• Genotype is the collective DNA sequence
• Organisms demonstrate ploidy which is the number of genome copies
• Yeast can thrive as haploids (one genome copy) or diploids
• More complex eukaryotes (like humans) are diploid, and sometimes polyploid
• Diploidy leads to a mixed population of available gene products
• Extra genome copies provide a "back-up" to protect against defective genes

Genetic Analysis

• Genetic analysis compares normal ("wild-type") organisms versus non-wild-type (mutant) organisms
• Forward genetics identifies genes based on observed mutant phenotypes
• Reverse genetics disrupts a gene of interest and observes the resulting phenotype
• Alleles are similar but different versions of a gene (such as wild-type and mutant)

Gene Mutation and Phenotypic Consequence

• Mutations are generally recessive or dominant
• In organisms with multiple genome copies, a mutation might appear in only one copy of a gene
• If the remaining wild-type gene maintains cell function, the mutation is recessive
• When the wild-type gene cannot compensate for a mutant gene, the mutation is dominant

Nature of the Mutations

Mutations can stem from small or large gene changes

• Mutations change in gene sequence and protein structure
• Mutations change regulatory regions of genes and change gene expression
• Null mutations eliminate gene function (loss of function mutation)
• Gain of function mutations are new/abnormal functions

Point Mutations

• The single nucleotide changes can alter the encoded amino acid (missense mutations)
• Single nucleotide changes can cause a premature stop codon (nonsense mutations)
• Single nucleotide changes don’t alter the encoded amino acid (silent mutations)

Mutation and Disease

• Somatic cell mutations affect the organism itself, while germline cell mutations affect later generations
• Mutations often cause disease; single-gene mutations cause monogenic diseases (i.e. phenylketonuria)
• Polygenic (multifactorial) diseases result from changes in several genes (i.e. Alzheimer's, diabetes)
• Mutations don't always lead to disease, but increase disease likelihood
• Penetrance is the percentage of people with the mutation that will develop the disease

Dynamic Genome and Evolution

• Genomes change due to DNA mutations
• In a population with several gene versions (alleles), all persist unless one performs better
• Natural selection preferentially allows the best version to persist
• Cumulative mutations + natural selection produces new organisms and life's diversity

DNA Sequence Comparison

• Similar DNA sequences reveal how closely related organisms are
• Genes for "core" processes are more similar
• Aligning sequences from many DNA regions shows how related organisms are
• Phylogenetic trees indicate relatedness

Three Domains in Life

• The length of the "branch" in phyllogenetic trees demonstrates how closely related organisms are

Model Organisms

• Model organisms facilitates research and understanding of biological processes
• All multicellular organisms are eukaryotic, but not all eukaryotes are multicellular
• S. pombe and S. cerevisiae are single-celled with highly diverged genomes
• Model organisms (like fungi S. pombe/S. cerevisiae and bacteria E. coli/B. subtilis) have furthered research into many biological processes
• Model organisms form testable hypotheses about biological systems

Model Organisms pt. 2

• Fast generation time and cultivated in the laboratory
• Many mutant fruit fly organisms (Drosophila melanogaster) with altered developmental pathways have been identified
• Nematode worms (Caenorthabditis elegans) have a relatively simple adult worm with only about 1,000somatic cells and completely known patterns of cell division inside of the embryo

Model Organisms pt. 3

• Model organisms helps to study morphological feature of development:
• the African clawed frog (Xenopus laevis), has large and easily manipulated eggs
• the House mouse(Mus musculus) & Zebrafish (Danio rerio)
• Plant: thale cress (Arabidopsis thaliana, 애기장대) has a short generation (about 6 weeks); small genome size; small enough to be grown in the laboratory; large number of seeds

Viruses

• Viruses have small nucleic acid genomes with a protein coat
• Viruses require a host to replicate
• Viruses are associated with organisms in huge quantities and different varieties
• Well studied viruses (such as bacteriophage Lambda and Simian virus 40) have been used as a model to understand transcription and replication

Nomenclature

• Molecular components are often conserved throughout the living world
• Historically different naming practices/independently discovered processes exist and genes are frequently named differently
• Wild-ytpe genes are written in uppercase and muatnts in lowercase in yeast. Italicize the gnes, and no italicize the proteins -URA3 (WT gene); ura3-52 (mutant gene); Ura3 (WT protein); ura3 (mutant protein)
• Homologous genes/proteins in different organisms may not have the same names while perofrmationg same function such as Sliding Clamp and Sliding proetin (E. Coli PCNA (eukaryotes)